Hopefully, this exercise will contribute to some actual work that you are trying to do in your research!
# Batch processing to create graphs for SelectPos
# load data ----------------------------------
library(ggplot2)
library(data.table)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:data.table':
##
## between, first, last
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
load("/Users/skogut/Desktop/Thesis/SelectPosVACC.rda")
SelectPos<- arrange(SelectPos, by= desc(Slope))
SelectPos$ERV<- gsub("X", "", SelectPos$ERV)
SelectPairs<- SelectPos[1:1000, 1:2]
SelectPairs$ERV<- gsub("\\.", "-", SelectPairs$ERV)
print(SelectPairs)
## ERV Transcript
## 1 727 ENST00000361381.2
## 2 727 ENST00000361453.3
## 3 K-32 ENST00000387347.2
## 4 727 ENST00000361567.2
## 5 2758 ENST00000361453.3
## 6 727 ENST00000361390.2
## 7 2758 ENST00000361381.2
## 8 727 ENST00000361335.1
## 9 2758 ENST00000361335.1
## 10 2758 ENST00000387347.2
## 11 4666 ENST00000387347.2
## 12 4666 ENST00000361453.3
## 13 2758 ENST00000361567.2
## 14 5110 ENST00000627981.1
## 15 2758 ENST00000361390.2
## 16 727 ENST00000361789.2
## 17 5109 ENST00000627981.1
## 18 4666 ENST00000361381.2
## 19 4666 ENST00000361335.1
## 20 727 ENST00000361624.2
## 21 2593 ENST00000627981.1
## 22 2758 ENST00000361789.2
## 23 4666 ENST00000361390.2
## 24 4666 ENST00000361567.2
## 25 5047 ENST00000627981.1
## 26 2758 ENST00000361624.2
## 27 2758 ENST00000389680.2
## 28 4851 ENST00000387347.2
## 29 4851 ENST00000361453.3
## 30 4641 ENST00000389680.2
## 31 4851 ENST00000361381.2
## 32 727 ENST00000361681.2
## 33 K-32 ENST00000361381.2
## 34 4666 ENST00000361789.2
## 35 4666 ENST00000361624.2
## 36 K-32 ENST00000389680.2
## 37 4851 ENST00000361335.1
## 38 4851 ENST00000361567.2
## 39 K-32 ENST00000361335.1
## 40 2758 ENST00000361899.2
## 41 4851 ENST00000361390.2
## 42 K-32 ENST00000361567.2
## 43 935 ENST00000387347.2
## 44 1716 ENST00000387347.2
## 45 3184 ENST00000387347.2
## 46 2758 ENST00000361681.2
## 47 4894 ENST00000387347.2
## 48 K-32 ENST00000361453.3
## 49 K-32 ENST00000361624.2
## 50 4606 ENST00000387347.2
## 51 4894 ENST00000361453.3
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## 53 4851 ENST00000361789.2
## 54 4851 ENST00000389680.2
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## 57 4894 ENST00000361381.2
## 58 4851 ENST00000361624.2
## 59 3184 ENST00000361381.2
## 60 2758 ENST00000361739.1
## 61 4894 ENST00000361335.1
## 62 727 ENST00000361851.1
## 63 3184 ENST00000361335.1
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## 65 4666 ENST00000361681.2
## 66 K-32 ENST00000361789.2
## 67 5110 ENST00000629969.1
## 68 4894 ENST00000361567.2
## 69 1393 ENST00000387347.2
## 70 4894 ENST00000361390.2
## 71 3184 ENST00000361390.2
## 72 3375 ENST00000387347.2
## 73 2758 ENST00000361851.1
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## 75 3184 ENST00000361567.2
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## 78 3375 ENST00000361453.3
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## 87 1393 ENST00000361453.3
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## 90 4666 ENST00000361851.1
## 91 935 ENST00000361453.3
## 92 4894 ENST00000361624.2
## 93 3184 ENST00000361624.2
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## 96 1393 ENST00000361381.2
## 97 4666 ENST00000514057.1
## 98 K-32 ENST00000361681.2
## 99 935 ENST00000389680.2
## 100 1716 ENST00000389680.2
## 101 1716 ENST00000361567.2
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## 103 5047 ENST00000629969.1
## 104 3375 ENST00000361335.1
## 105 935 ENST00000361381.2
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## 122 UID-51 ENST00000387347.2
## 123 4118 ENST00000361335.1
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## 182 4894 ENST00000361739.1
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## 185 W-117 ENST00000222553.7
## 186 727 ENST00000421673.6
## 187 1079 ENST00000361381.2
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## 189 4894 ENST00000361851.1
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## 194 1393 ENST00000361681.2
## 195 935 ENST00000361899.2
## 196 4606 ENST00000361789.2
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## 198 4606 ENST00000361335.1
## 199 3184 ENST00000361851.1
## 200 5047 ENST00000331825.10
## 201 1079 ENST00000361453.3
## 202 3864 ENST00000361335.1
## 203 727 ENST00000617585.1
## 204 4666 ENST00000560711.1
## 205 4894 ENST00000514057.1
## 206 1716 ENST00000361899.2
## 207 3184 ENST00000514057.1
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## 209 2758 ENST00000577894.1
## 210 2758 ENST00000555997.1
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## 212 3723 ENST00000550536.5
## 213 W-117 ENST00000457540.1
## 214 4666 ENST00000577894.1
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## 216 3864 ENST00000361567.2
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## 219 3375 ENST00000514057.1
## 220 K-32 ENST00000518964.5
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# Transcripts<- fread("/Users/skogut/Desktop/Thesis/Transcripts_normalized_counts_WF.csv")
# ERV<- fread("/Users/skogut/Desktop/Thesis/ERV_normalized_counts_WF.csv")
Transcripts<- readRDS("Transcripts.RDS")
ERV<- readRDS("ERV.RDS")
# saveRDS(Transcripts, "Transcripts.RDS")
# saveRDS(ERV, "ERV.RDS")
dir.create("PositiveERV_Trans/")
## Warning in dir.create("PositiveERV_Trans/"): 'PositiveERV_Trans' already exists
# Create files ----------------------------------
# two sets of counts per file: 1 set from ERV, transcript per top 1000 pairs
########################################################
# FUNCTION file_builder
# description: creates a sest of random files for regression
# inputs: file_n = number f files to create
# file_folder = name of folder for random file
# file_size = c(min,max) number of rows in file
# file_NA= average number of NA values per column
# outputs: creates a set of random files
# -----------------------------------------------------
file_builder <- function(file_n=1000,
file_folder= "PositiveERV_Trans/",
ERVdata= 1:1000,
Transcriptdata= 1:1000,
SelectPairs= 1:1000) {
for (i in 1:nrow(SelectPairs)) {
var_x<- SelectPairs[i,1] # ERV
var_y<-SelectPairs[i,2] # Transcript
df<- data.frame(var_x = ERVdata[[ which(colnames(ERVdata)== var_x)]], var_y= Transcriptdata[[which(colnames(Transcriptdata)== var_y)]]) # bind into a data frame
colnames(df)<- c(var_x, var_y)
print(df)
# create label for file name with padded zeroes
file_label<- paste(file_folder, "PairFile",
formatC(i,
width=3,
format= "d",
flag= "0"),
".csv",
sep="")
# set up data file and incorporate time stamp and minimal meta data
write.table(cat("# Simulated random data filefor batch processing", "\n",
"# timestamp: ", as.character(Sys.time()),
"\n",
"# SEK", "\n",
"#----------------------------", "\n",
"\n",
file=file_label,
row.names= "",
col.names= "",
sep= "") )
# now add the data frame
write.table(x=df,
file= file_label,
sep=",",
row.names= FALSE,
append=TRUE)
}
} # end of file_builder
########################################################
# Create regression function/ graphing function ----------------------------------
########################################################
# FUNCTION reg_stats
# description: fits liner model extract m stats
# inputs: 2column data frame (x and y)
# outputs: slope, p-value, and r2
# -----------------------------------------------------
reg_stats <- function(d= NULL) {
if( is.null(d)){
x_var<- runif(10)
y_var<- runif(10)
d<- data.frame(x_var, y_var) }
.<- lm(data=d, d[,2]~d[,1])
.<- summary(.)
stats_list<- list(Slope=.$coefficients[2,1],
pval= .$coefficients[2,4],
r2=.$r.squared)
return(stats_list)
} # end of reg_stats
########################################################
# test
#######################################################
#global
file_folder<- "PositiveERV_Trans/"
n_files<- 100
file_out<- "StatsSummaryHW.csv"
file_names<- list.files(path= file_folder)
#######################################################
# running file builder to build files
file_builder(ERVdata = ERV, Transcriptdata = Transcripts, SelectPairs = SelectPairs)
# batch process by looping through individual files ----------------------------------
# create data frame to hold summary stats
ID<- seq_along(file_names)
file_name<- file_names
slope<- rep(NA, length(file_names))
pval<- rep(NA, length(file_names))
r2<- rep(NA, length(file_names))
stats_out<- data.frame(ID, file_name, slope, pval, r2)
# batch process by looping through individual files
for(i in seq_along(file_names)) {
data<- read.table(file=paste(file_folder, file_names[i],
sep=""),
sep=",",
header= TRUE)
.<- reg_stats(d=data) # pull out regression stats from clean file
stats_out[i,3:5]<- unlist(.) # unlist, copy into last three cols
}
# set up an output file and incorporate time stamp and minimal metadata
write.table(cat( "# Summary stats for",
"batch processing of regression models",
"\n",
"# timestamp: ", as.character(Sys.time()),
"\n",
file= file_out,
row.names= "",
col.names="",
sep= ""))
## ""
# set up an output file and incorporate time stamp and minimal metadata
# now add the data frame
write.table(x=stats_out,
file=file_out,
row.names=FALSE,
col.names=TRUE,
sep= ",",
append=TRUE)
## Warning in write.table(x = stats_out, file = file_out, row.names = FALSE, :
## appending column names to file
file_out<- "StatsSummaryHW.csv"
# arranging data to find something meaningful
stats_out<- arrange(stats_out, desc(r2))
head(stats_out)
## ID file_name slope pval r2
## 1 950 PairFile949.csv 842.8526 2.313595e-52 0.9844926
## 2 824 PairFile823.csv 897.8977 1.133303e-27 0.8821019
## 3 579 PairFile578.csv 1266.0763 1.569202e-27 0.8807268
## 4 976 PairFile975.csv 789.6071 2.540270e-27 0.8786620
## 5 796 PairFile795.csv 924.5246 5.063990e-27 0.8756426
## 6 999 PairFile998.csv 777.0859 9.411610e-27 0.8728661
# plotting quick scatterplots to look for outliers, in the top 50 pairs when ordered by r2
for (i in 1:50) {
data<- read.table(file=paste(file_folder, stats_out$file_name[i],
sep=""),
sep=",",
header= TRUE)
p<- qplot(x=data[,1],
y=data[,2],
geom= c("smooth", "point"), method= "lm",
xlim= c(0, 25),
ylim= c(0,10000))
print(i)
print(p)
Sys.sleep(1.5)
}
## Warning: Ignoring unknown parameters: method
## [1] 1
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 2
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 3
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 4
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 5
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 6
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 7
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 8
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 9
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 10
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 11
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 44 rows containing non-finite values (stat_smooth).
## Warning: Removed 44 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 12
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 13
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 14
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 18 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 15
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 16
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 37 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 17
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 19 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 18
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 40 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 19
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 20
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 28 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 21
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 22
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 23
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 24
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 39 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_smooth).
## Warning: Removed 39 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 25
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 10 rows containing non-finite values (stat_smooth).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 26
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 41 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 27
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 33 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 28
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 35 rows containing non-finite values (stat_smooth).
## Warning: Removed 35 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 29
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 15 rows containing non-finite values (stat_smooth).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 30
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 3 rows containing non-finite values (stat_smooth).
## Warning: Removed 3 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 31
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 32
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 33
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 22 rows containing non-finite values (stat_smooth).
## Warning: Removed 22 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 34
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 35
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 11 rows containing non-finite values (stat_smooth).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 36
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 53 rows containing non-finite values (stat_smooth).
## Warning: Removed 53 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 37
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 38
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 39
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 10 rows containing non-finite values (stat_smooth).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 40
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 45 rows containing non-finite values (stat_smooth).
## Warning: Removed 45 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 41
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 44 rows containing non-finite values (stat_smooth).
## Warning: Removed 44 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 42
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 43
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 7 rows containing non-finite values (stat_smooth).
## Warning: Removed 7 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 44
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 7 rows containing non-finite values (stat_smooth).
## Warning: Removed 7 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 45
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 46
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 47
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 48
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 11 rows containing non-finite values (stat_smooth).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 49
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 52 rows containing non-finite values (stat_smooth).
## Warning: Removed 52 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method
## [1] 50
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).